How to access genomic information using Ensembl

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How to access genomic information using Ensembl
Damian Smedley and Xosé Fernández Ensembl
Project European Bioinformatics
Institute Cambridge, UK
November 2004
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Schedule
Today Introduction to the Ensembl
system Hands-on examples to introduce the
system Evaluating genes and transcripts Variation
in Ensembl (SNPs, haplotypes) Tomorrow Data
mining with EnsMart Comparative genomics and
proteomics in Ensembl BioMart Advanced topics
(Upload your own data, DAS)
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Our goal
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Assembly
Other ordering data
non-redundant, virtual contig view
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Mapping and Sequencing the human genome
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Status of the human sequence

• finished red /orange
• 96 (99.999 accurate)
• 30-40 repetitive elements (eg Alpha satellite,
  Alu repeats)
• All known genes, correctly identified (99.74)
• heterochromatin
• 4 grey

Assembled draft sequence totals 2.85 Gb
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Human genome Current status

• 22,287 'gene loci defined, consisting of 19,599
  protein-coding genes in the human genome and
  2,188 DNA additional segments predicted to be
  protein-coding genes
• 1183 genes were born in the last 60-100 My
• 30 genes died in a similar time period

Finishing the euchromatic sequence of the human
genome, Nature 431931-45 (2004)
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Ensembl - project aims

• funded to provide metazoan genomes to the world
• aims to provide the worlds best automated genome
  annotation
• a leading group for human and mouse analysis
• all software, data and results freely available

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Ensembl - project background

• group split between EBI and Sanger
• mainly Wellcome Trust funded
• largest dedicated compute in biology in Europe
• developer community gt 100 people, including
  companies

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Ensembl Open source

• Freely-available
• Community development.
• gt51 Ensembl installs worldwide.
• Both public and commercial,
• e.g. Gramene (CSHL)
• Fugu-sg (ICMB)
• Ciona-sg (Temasek)

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Ensembl
Supporting Databases
Final DB
Analysis DB
CPU
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Genome browsingwhy present the whole genome?

• Explore what is in a chromosome region
• See features in and around a specific gene
• Search retrieve across the whole genome
• Investigate genome organization
• Compare to other genomes

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Genome browsers

• Ensembl public site installable system

• UCSC Human Genome Browser

• NCBI Map Viewer

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Introduction to the Ensembl web site
Ensembl
takes genomic sequence assemblies human build 34,
mouse, rat, Fugu,mosquito
adds annotation and links automated process
presents all the data on a web site
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Annotation genes
Known genes
Novel genes

• how to predict?
• require evidence
• transcripts(s)?
• protein(s)?
• orthologues?
• attach useful links

• where?
• genomic structure?
• transcripts(s)?
• protein(s)?
• orthologues?
• attach useful links

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Annotation other features

• markers and SNPs
• cytogenetic bands
• repeated sequences
• ESTs other sequence records
• where do they show sequence similarity?
• regions homologous to other species

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How to get started

• Species homepage
• Site map
• Map View
• Text search
• BLAST
• SSAHA
• Disease View

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Homepage
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Site map
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MapView
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BLAST and SSAHA
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BLAST and SSAHA
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Regions, maps and markers
ContigView CytoView SyntenyView MultiContigView
MarkerView SNPView
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EnsemblContigView
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ContigView close-up
Pop-up menu
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ContigView - Chromosome 20 close-up
Manual annotation via Vega
Forward strand
Ensembl predictions
Reverse strand
Ensembl EST-based predictions
Other chromosomes with manual annotation from
http//vega.sanger.ac.uk 6, 7, 9, 10, 13, 14,
20, 22, X
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CytoView
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GeneSNPView
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MarkerView
SNPView
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SyntenyView
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MultiContigView
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Genes gene products
GeneView TransView ExonView ProteinView
FamilyView DomainView
GOView DiseaseView
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EnsemblGeneView
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TransView
ExonView
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ProteinView
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FamilyView
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GOView
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DiseaseView
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Data retrieval
EnsMart
Export View
Data sets on ftp site MySQL queries of
databases Perl API access to databases
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ExportView
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EnsMart
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Mouse differences

• Genomic sequence assembly based on whole genome
  shotgun, with finished stitched BACs
• BACs are shown in CytoView (FPC map), but for
  most no sequence is available

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MouseCytoView
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Help!

• context sensitive help pages - click
• access other documentation via generic home page
• email the helpdesk

HelpDesk / Suggestions
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Thanks
Ensembl Team
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Ensembl Team
November 2004